Variant report

Variant	rs783394
Chromosome Location	chr6:106988018-106988019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:106987044-106988289	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:106987895-106988022	MCF-7	breast:	n/a	n/a
3	POLR2A	chr6:106987615-106988255	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:106987686-106988214	GM12891	blood:	n/a	n/a
5	SPI1	chr6:106987917-106988347	HL-60	blood:	n/a	chr6:106988016-106988023
6	POLR2A	chr6:106987824-106988173	GM12878	blood:	n/a	n/a
7	MYC	chr6:106987952-106988196	NB4	blood:	n/a	n/a
8	POLR2A	chr6:106987598-106988211	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:106987666-106988376	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:106987821-106988165	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:106987633-106988377	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:106987848-106988135	MCF-7	breast:	n/a	n/a
13	POLR2A	chr6:106987012-106988253	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
AIM1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13202942	0.87[ASW][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap]
rs13218960	0.87[ASW][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap]
rs2792466	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4946760	1.00[ASN][1000 genomes]
rs6941640	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs783390	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs783392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs783393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320173	0.87[ASW][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap]
rs9320174	0.87[ASW][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap]
rs9486382	0.81[CEU][hapmap]
rs9486383	0.87[ASW][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs783394	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs783394	QRSL1	cis	cerebellum	SCAN
rs783394	QRSL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-106991000	Weak transcription	Spleen	Spleen
3	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
4	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:106978800-106993800	Weak transcription	NHLF	lung
8	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
9	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
10	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:106982800-106993200	Weak transcription	HUVEC	blood vessel
12	chr6:106983400-106989000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:106983400-106989800	Strong transcription	Dnd41	blood
14	chr6:106984000-106989200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:106984400-106990200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:106984600-106988600	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:106984800-106989800	Strong transcription	NHEK	skin
18	chr6:106985000-106988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:106985000-106993800	Weak transcription	NH-A	brain
20	chr6:106985400-106988200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:106985800-106988600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:106985800-106988800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
24	chr6:106986000-106988200	Enhancers	Placenta	Placenta
25	chr6:106986200-106992000	Strong transcription	Fetal Intestine Small	intestine
26	chr6:106986200-106993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:106986200-106994000	Weak transcription	Stomach Mucosa	stomach
28	chr6:106986400-106989200	Weak transcription	Fetal Thymus	thymus
29	chr6:106986400-106993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:106986400-106995000	Weak transcription	Thymus	Thymus
32	chr6:106986600-106989000	Weak transcription	Fetal Intestine Large	intestine
33	chr6:106986800-106988600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:106986800-106989000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:106986800-106989000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:106986800-106991200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:106986800-106991200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:106986800-106992000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:106986800-106994400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:106987000-106988200	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr6:106987000-106988200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:106987000-106989000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:106987000-106989800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:106987000-106989800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:106987000-106992200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:106987000-106993600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:106987200-106988800	Enhancers	Hela-S3	cervix
48	chr6:106987200-106988800	Enhancers	HepG2	liver
49	chr6:106987400-106992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:106987400-106993800	Strong transcription	Primary T cells fromperipheralblood	blood

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